SMTL ID : 9kbg.1

The structure of B19V NS1_2-570/AMPPNP

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-12-mer

Ligands

12 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.1: 16 residues within 4Å: Chain A: P.329, S.330, T.331, G.332, K.333, T.334, N.335, E.372, N.414, C.447, S.448, P.449, M.451, G.452, L.453 Ligands: MG.2 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:S.330, A:T.331, A:T.331, A:G.332, A:K.333, A:K.333, A:K.333, A:T.334, A:N.335, A:E.372, A:N.414, A:N.414, A:C.447, A:G.452 Water bridges: A:T.334, A:T.334, A:T.334 ANP.3: 15 residues within 4Å: Chain B: P.329, S.330, T.331, G.332, K.333, T.334, N.335, N.414, C.447, S.448, P.449, M.451, G.452, L.453 Ligands: MG.4 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:S.330, B:T.331, B:T.331, B:G.332, B:K.333, B:K.333, B:T.334, B:T.334, B:N.335, B:N.414, B:N.414, B:S.448 Water bridges: B:T.334, B:T.412 ANP.5: 16 residues within 4Å: Chain C: P.329, S.330, T.331, G.332, K.333, T.334, N.335, E.372, N.414, S.448, P.449, D.450, M.451, G.452, L.453 Ligands: MG.6 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:S.330, C:T.331, C:G.332, C:K.333, C:K.333, C:T.334, C:T.334, C:N.335, C:E.372, C:N.414, C:N.414, C:P.449, C:M.451 ANP.7: 14 residues within 4Å: Chain D: P.329, S.330, T.331, G.332, K.333, T.334, N.335, N.414, S.448, P.449, M.451, G.452, L.453 Ligands: MG.8 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:S.330, D:T.331, D:G.332, D:K.333, D:K.333, D:T.334, D:T.334, D:N.335, D:N.335, D:N.414, D:N.414, D:S.448 Water bridges: D:T.334 ANP.9: 14 residues within 4Å: Chain E: P.329, S.330, T.331, G.332, K.333, T.334, N.335, N.414, C.447, S.448, M.451, G.452, L.453 Ligands: MG.10 14 PLIP interactions: 14 interactions with chain E Hydrogen bonds: E:S.330, E:T.331, E:T.331, E:G.332, E:K.333, E:K.333, E:T.334, E:T.334, E:N.335, E:N.414 Water bridges: E:T.334, E:T.334, E:T.334, E:T.334 ANP.11: 14 residues within 4Å: Chain F: P.329, S.330, T.331, G.332, K.333, T.334, N.335, N.414, C.447, S.448, P.449, M.451, L.453 Ligands: MG.12 13 PLIP interactions: 13 interactions with chain F Hydrogen bonds: F:S.330, F:T.331, F:G.332, F:K.333, F:K.333, F:T.334, F:N.335, F:E.372, F:N.414, F:N.414, F:S.448 Water bridges: F:T.334, F:T.334 ANP.13: 15 residues within 4Å: Chain G: P.329, S.330, T.331, G.332, K.333, T.334, N.335, E.372, N.414, S.448, P.449, M.451, G.452, L.453 Ligands: MG.14 15 PLIP interactions: 15 interactions with chain G Hydrogen bonds: G:S.330, G:T.331, G:G.332, G:K.333, G:K.333, G:K.333, G:T.334, G:T.334, G:N.335, G:N.414, G:P.449, G:L.453 Water bridges: G:T.334, G:T.334, G:T.334 ANP.15: 17 residues within 4Å: Chain H: P.328, P.329, S.330, T.331, G.332, K.333, T.334, N.335, E.372, N.414, C.447, S.448, P.449, M.451, G.452, L.453 Ligands: MG.16 15 PLIP interactions: 15 interactions with chain H Hydrogen bonds: H:S.330, H:T.331, H:G.332, H:K.333, H:K.333, H:K.333, H:T.334, H:T.334, H:T.334, H:N.335, H:N.335, H:E.372, H:N.414, H:N.414, H:C.447 ANP.17: 17 residues within 4Å: Chain I: P.329, S.330, T.331, G.332, K.333, T.334, N.335, E.372, N.414, C.447, S.448, P.449, D.450, M.451, G.452, L.453 Ligands: MG.18 15 PLIP interactions: 15 interactions with chain I Hydrogen bonds: I:S.330, I:T.331, I:G.332, I:K.333, I:K.333, I:T.334, I:T.334, I:N.335, I:E.372, I:N.414, I:N.414, I:P.449, I:M.451, I:G.452 Water bridges: I:T.334 ANP.19: 12 residues within 4Å: Chain J: P.329, S.330, T.331, G.332, K.333, T.334, N.335, N.414, S.448, P.449, L.453 Ligands: MG.20 10 PLIP interactions: 10 interactions with chain J Hydrogen bonds: J:S.330, J:T.331, J:G.332, J:K.333, J:K.333, J:T.334, J:N.335, J:N.335, J:N.414, J:S.448 ANP.21: 16 residues within 4Å: Chain K: P.329, S.330, T.331, G.332, K.333, T.334, N.335, E.372, N.414, C.447, S.448, P.449, M.451, G.452, L.453 Ligands: MG.22 16 PLIP interactions: 16 interactions with chain K Hydrogen bonds: K:S.330, K:T.331, K:G.332, K:K.333, K:K.333, K:T.334, K:N.335, K:E.372, K:N.414, K:S.448 Water bridges: K:T.334, K:T.334, K:T.334, K:T.334, K:E.372, K:E.372 ANP.23: 15 residues within 4Å: Chain L: P.329, S.330, T.331, G.332, K.333, T.334, N.335, E.372, N.414, S.448, P.449, M.451, G.452, L.453 Ligands: MG.24 10 PLIP interactions: 10 interactions with chain L Hydrogen bonds: L:S.330, L:T.331, L:G.332, L:K.333, L:K.333, L:T.334, L:N.335, L:E.372, L:N.414, L:S.448

12 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: T.334 Ligands: ANP.1 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:T.334, H2O.1, H2O.1, H2O.1 MG.4: 2 residues within 4Å: Chain B: T.334 Ligands: ANP.3 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:T.334, H2O.1, H2O.1, H2O.1 MG.6: 2 residues within 4Å: Chain C: T.334 Ligands: ANP.5 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:T.334, H2O.1, H2O.1, H2O.1 MG.8: 2 residues within 4Å: Chain D: T.334 Ligands: ANP.7 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:T.334, H2O.1, H2O.1, H2O.1 MG.10: 2 residues within 4Å: Chain E: T.334 Ligands: ANP.9 4 PLIP interactions: 1 interactions with chain E, 3 Ligand-Water interactions Metal complexes: E:T.334, H2O.1, H2O.1, H2O.1 MG.12: 2 residues within 4Å: Chain F: T.334 Ligands: ANP.11 3 PLIP interactions: 1 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:T.334, H2O.1, H2O.1 MG.14: 2 residues within 4Å: Chain G: T.334 Ligands: ANP.13 3 PLIP interactions: 1 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:T.334, H2O.1, H2O.1 MG.16: 3 residues within 4Å: Chain H: T.334, E.372 Ligands: ANP.15 2 PLIP interactions: 1 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:T.334, H2O.1 MG.18: 2 residues within 4Å: Chain I: T.334 Ligands: ANP.17 4 PLIP interactions: 1 interactions with chain I, 3 Ligand-Water interactions Metal complexes: I:T.334, H2O.1, H2O.1, H2O.1 MG.20: 2 residues within 4Å: Chain J: T.334 Ligands: ANP.19 3 PLIP interactions: 1 interactions with chain J, 2 Ligand-Water interactions Metal complexes: J:T.334, H2O.1, H2O.1 MG.22: 3 residues within 4Å: Chain K: T.334, E.372 Ligands: ANP.21 4 PLIP interactions: 1 interactions with chain K, 3 Ligand-Water interactions Metal complexes: K:T.334, H2O.2, H2O.2, H2O.2 MG.24: 4 residues within 4Å: Chain L: T.334, D.371, E.372 Ligands: ANP.23 1 PLIP interactions: 1 interactions with chain L Metal complexes: L:T.334

Links

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Citation

Zhang, Y. et al., Structural and functional studies of the main replication protein NS1 of human parvovirus B19. Nucleic Acids Res. (2025)

Release Date

2025-07-09

Peptides

Non-structural protein 1: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

Non-structural protein 1

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